Sydney - Swimming Australia said on Wednesday it does not endorse James Magnussen's new training programme but will continue to provide the world champion swimmer with financial support.
Magnussen, 23, a two-time 100m freestyle world champion, ended his four-year partnership with coach Brant Best in September and is training under untested young coaches Mitch and Lach Falvey as he prepares for the 2016 Rio Olympics.
Magnussen, known as 'The Missile', has been at loggerheads with Swimming Australia's head coach Jacco Verhaeren and high performance director Michael Scott over his plans to train under the Falvey brothers in Sydney.
"From the outset Swimming Australia has wanted what we believe is best for James to fulfil his potential and to be ready for next year's world championships and the 2016 Olympics," Scott said in a statement.
"Our head coach Jacco Verhaeren, the man who guided (Dutchman) Pieter van den Hoogenband to three Olympic gold medals, two in the 100m freestyle, has been heavily involved with James and his team and has provided them with his advice.
"We do not support the training environment James has chosen going forward and there are a range of factors that have led us to that decision and we are not about to go into them.
"But in saying that we have nothing against the young coaches Mitch and Lach Falvey - at the end of the day we respect James' right to make his own decision - although we haven't got to agree with it."
Scott added that Swimming Australia's financial support for Magnussen would be targeted at specific gaps Verhaeren has identified.